Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M. tuberculosis). Tuberculosis is contagious and is spread by airborne bacilli from the lungs of an infectious person. Approximately one-third of the world's population are carriers of M. tuberculosis, most of whom are asymptomatic. Approximately 5-10% of those infected with M. tuberculosis will become sick or infectious at some point in their lifetime. In the United States, nearly 15,000 new cases of tuberculosis were reported in 2003. The incidence is much higher in South East Asia and parts of Africa.
Persons infected with both the HIV virus and M. tuberculosis are particularly susceptible to developing tuberculosis. The weakened immune system of an HIV-infected increases the likelihood the individual will become sick with tuberculosis. Presently, it is estimated that about 15 million patients are infected by both the M. tuberculosis and HIV and having tuberculosis accounts for approximately 13% of deaths in AIDS patients.
The genus Mycobacterium contains approximately 50 species. The best known and widest spread diseases caused by mycobacteria are leprosy, caused by M. leprae, and tuberculosis caused by M. tuberculosis. Most other mycobacteria normally occur only as environmental saprophytes. However, saprophytic mycobacterial species also cause opportunist diseases, which happens often, but not exclusively, in individuals suffering from suppressed immune systems, such as AIDS patients or individuals undergoing immuno-suppression therapy. The opportunist strains comprise the slow-growing species M. avium, and the closely related M. intracellulare and M. scrofulaceum (often together referred to as the MAIS complex), M. kansai, M. marinum and M. ulcerans, and the fast-growing species M. chelonae and M. fortultum. Although quite rare in the Western world for several decades, the occurrence of opportunist mycobacterial diseases and tuberculosis has shown a significant increase with the incidence of AIDS. Further, it has been reported that mycobacteria are involved in the etiology of a plurality of other diseases, such as sarcoidosis and Crohn's disease, as well as different auto-immune diseases, such as auto-immune dermatitis, rheumatoid arthritis and diabetes. It has been suggested that this role can be attributed to a structural mimicry between epitopes of mycobacteria and those of the host organism.
A rapid clinical diagnosis of M. tuberculosis infection has important clinical and therapeutic implications because of the morbidity associated with the disease and the possibility for further spread of this disease. Although presumptive diagnosis of tuberculosis can be made on the basis of patient histories, clinical and radiological findings, and the presence of acid-fast bacilli in patient specimens, the isolation of M. tuberculosis is required for the definitive diagnosis of tuberculosis. Smear tests of sputum samples are considered the least sensitive technique for diagnosis of TB because the estimated number of bacteria required for a positive test is relatively high. Routine cultures are cumbersome and time-consuming.
Early efforts aimed at differentiating among strains of M. tuberculosis on a nucleic acid level largely failed until the discovery of polymorphic sites within repetitive sequences of the genome were identified. IS6110 is a transposable element that is currently the most widely used marker for differentiating strains of M. tuberculosis (Murray and Nardell, Bulletin of the World Health Organization 80(6):477-482, 2002). IS6110 is found in multiple copies throughout the genome of M. tuberculosis and is preferentially inserted into a sequence of DNA termed the IS6110 preferential locus, ipl. The ipl locus is a stretch of 267 nucleotides that contains 6 sites for IS6110 insertion. The ipl locus corresponds to the first 267 nucleotides of GenBank Accession No. X95799 (SEQ ID NO:4); no insertion sites have been found in the 3′-flanking region (nucleotides 268 through 650 of SEQ ID NO:4) of this sequence. (Fang and Forbes, J Clin Microbiol 35:479-81, 1997; Fang et al., J Bacteriol 181:1014-20, 1999; Fang et al., J Bacteriol 181:1021-4, 1999).
A Mycobacterium tuberculosis (MT) complex of organisms has been identified and includes organisms which are closely related species of the genus Mycobacterium and which cause a tuberculosis-like syndrome. MT complex organisms share a high degree of evolutionary conservation and include M. tuberculosis, M. bovis, M. bovis BCG, M. Africanum, M. Microti, and M. canettii. 
Polymerase chain reaction (“PCR”) has been widely utilized to improve the sensitivity of standard hybridization methods. U.S. Pat. No. 6,815,165 discloses a method and kit which uses PCR to specifically detect M. tuberculosis DNA in a test sample. Hybridization assays using self-quenching fluorescence probes with and/or without internal controls for detection of nucleic acid application products are known in the art, for example, U.S. Pat. Nos. 6,258,569; 6,030,787; 5,952,202; 5,876,930; 5,866,336; 5,736,333; 5,723,591; 5,691,146; and 5,538,848. In addition, the detection of M. tuberculosis using Real-time PCR (Taqman systems) has been described by Desjardin et al., J. Clin. Microbiol. 36(7):1964-1968, 1998.